napari-memmap-tiff 1.0.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- napari_memmap_tiff-1.0.0/.github/workflows/test_and_deploy.yml +91 -0
- napari_memmap_tiff-1.0.0/.gitignore +84 -0
- napari_memmap_tiff-1.0.0/.napari-hub/DESCRIPTION.md +7 -0
- napari_memmap_tiff-1.0.0/.napari-hub/config.yml +9 -0
- napari_memmap_tiff-1.0.0/.pre-commit-config.yaml +27 -0
- napari_memmap_tiff-1.0.0/LICENSE +22 -0
- napari_memmap_tiff-1.0.0/MANIFEST.in +5 -0
- napari_memmap_tiff-1.0.0/PKG-INFO +138 -0
- napari_memmap_tiff-1.0.0/README.md +75 -0
- napari_memmap_tiff-1.0.0/pyproject.toml +121 -0
- napari_memmap_tiff-1.0.0/setup.cfg +4 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/__init__.py +7 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/_tests/__init__.py +0 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/_tests/test_widget.py +12 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/_version.py +21 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/_widget.py +56 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff/napari.yaml +14 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/PKG-INFO +138 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/SOURCES.txt +22 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/dependency_links.txt +1 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/entry_points.txt +2 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/requires.txt +13 -0
- napari_memmap_tiff-1.0.0/src/napari_memmap_tiff.egg-info/top_level.txt +1 -0
- napari_memmap_tiff-1.0.0/tox.ini +33 -0
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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: tests
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on:
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push:
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branches:
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tags:
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pull_request:
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branches:
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jobs:
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test:
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name: ${{ matrix.platform }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.platform }}
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timeout-minutes: 30
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strategy:
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matrix:
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platform: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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- name: Set up Python ${{ matrix.python-version }}
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with:
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python-version: ${{ matrix.python-version }}
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# these libraries enable testing on Qt on linux
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git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
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powershell gl-ci-helpers/appveyor/install_opengl.ps1
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# setup-miniconda: https://github.com/conda-incubator/setup-miniconda
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# and
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# this runs the platform-specific tests declared in tox.ini
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uses: aganders3/headless-gui@v2
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run: python -m tox
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uses: codecov/codecov-action@v3
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deploy:
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# github secrets (see readme for details)
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needs: [test]
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runs-on: ubuntu-latest
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if: contains(github.ref, 'tags')
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pip install -U setuptools setuptools_scm wheel twine build
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
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# C extensions
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build/
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dist/
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downloads/
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When installed and enabled in the options, it adds an option that when enabled
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will make napari load tiffs via memory mapping instead of fully into RAM.
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That is, `.tif` and `.tiff` files will be loaded into memory using memory
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mapping, which loads the data directly from disk instead of loading the file
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at once into RAM. This is beneficial for large files that may not fit into
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available RAM.
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The MIT License (MIT)
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Copyright (c) 2025 Matthew Einhorn
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Metadata-Version: 2.4
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Name: napari-memmap-tiff
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Version: 1.0.0
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Summary: When installed and enabled in the options, it adds an option that when enabled will make napari load tiffs via memory mapping instead of fully into RAM.
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Author: Matthew Einhorn
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Author-email: matt@einhorn.dev
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License:
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The MIT License (MIT)
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Copyright (c) 2025 Matthew Einhorn
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Project-URL: Bug Tracker, https://github.com/matham/napari-memmap-tiff/issues
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Project-URL: Documentation, https://github.com/matham/napari-memmap-tiff#README.md
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Project-URL: Source Code, https://github.com/matham/napari-memmap-tiff
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Project-URL: User Support, https://github.com/matham/napari-memmap-tiff/issues
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Framework :: napari
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Topic :: Scientific/Engineering :: Image Processing
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy
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Requires-Dist: magicgui
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Requires-Dist: qtpy
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Requires-Dist: scikit-image
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Requires-Dist: tifffile
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Provides-Extra: testing
|
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Requires-Dist: tox; extra == "testing"
|
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Requires-Dist: pytest; extra == "testing"
|
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Requires-Dist: pytest-cov; extra == "testing"
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Requires-Dist: pytest-qt; extra == "testing"
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Requires-Dist: napari; extra == "testing"
|
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Requires-Dist: pyqt5; extra == "testing"
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Dynamic: license-file
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# napari-memmap-tiff
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[](https://github.com/matham/napari-memmap-tiff/raw/main/LICENSE)
|
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[](https://pypi.org/project/napari-memmap-tiff)
|
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[](https://python.org)
|
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[](https://github.com/matham/napari-memmap-tiff/actions)
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[](https://codecov.io/gh/matham/napari-memmap-tiff)
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[](https://napari-hub.org/plugins/napari-memmap-tiff)
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[](https://napari.org/stable/plugins/index.html)
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[](https://github.com/copier-org/copier)
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When installed and enabled in the options, it adds an option that when enabled
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will make napari load tiffs via memory mapping instead of fully into RAM.
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That is, `.tif` and `.tiff` files will be loaded into memory using memory
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mapping, which loads the data directly from disk instead of loading the file
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+
at once into RAM. This is beneficial for large files that may not fit into
|
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available RAM.
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+
----------------------------------
|
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This [napari] plugin was generated with [copier] using the [napari-plugin-template].
|
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+
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<!--
|
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+
Don't miss the full getting started guide to set up your new package:
|
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+
https://github.com/napari/napari-plugin-template#getting-started
|
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|
+
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and review the napari docs for plugin developers:
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https://napari.org/stable/plugins/index.html
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-->
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## Installation
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You can install `napari-memmap-tiff` via [pip]:
|
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pip install napari-memmap-tiff
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To install latest development version :
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pip install git+https://github.com/matham/napari-memmap-tiff.git
|
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
|
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|
+
the coverage at least stays the same before you submit a pull request.
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## License
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Distributed under the terms of the [MIT] license,
|
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"napari-memmap-tiff" is free and open source software
|
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## Issues
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+
If you encounter any problems, please [file an issue] along with a detailed description.
|
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+
[napari]: https://github.com/napari/napari
|
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[copier]: https://copier.readthedocs.io/en/stable/
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[@napari]: https://github.com/napari
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[MIT]: http://opensource.org/licenses/MIT
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[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
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+
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
|
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+
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
|
|
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|
+
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
|
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+
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
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[napari-plugin-template]: https://github.com/napari/napari-plugin-template
|
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|
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[file an issue]: https://github.com/matham/napari-memmap-tiff/issues
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[napari]: https://github.com/napari/napari
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[tox]: https://tox.readthedocs.io/en/latest/
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[pip]: https://pypi.org/project/pip/
|
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[PyPI]: https://pypi.org/
|
|
@@ -0,0 +1,75 @@
|
|
|
1
|
+
# napari-memmap-tiff
|
|
2
|
+
|
|
3
|
+
[](https://github.com/matham/napari-memmap-tiff/raw/main/LICENSE)
|
|
4
|
+
[](https://pypi.org/project/napari-memmap-tiff)
|
|
5
|
+
[](https://python.org)
|
|
6
|
+
[](https://github.com/matham/napari-memmap-tiff/actions)
|
|
7
|
+
[](https://codecov.io/gh/matham/napari-memmap-tiff)
|
|
8
|
+
[](https://napari-hub.org/plugins/napari-memmap-tiff)
|
|
9
|
+
[](https://napari.org/stable/plugins/index.html)
|
|
10
|
+
[](https://github.com/copier-org/copier)
|
|
11
|
+
|
|
12
|
+
When installed and enabled in the options, it adds an option that when enabled
|
|
13
|
+
will make napari load tiffs via memory mapping instead of fully into RAM.
|
|
14
|
+
|
|
15
|
+
That is, `.tif` and `.tiff` files will be loaded into memory using memory
|
|
16
|
+
mapping, which loads the data directly from disk instead of loading the file
|
|
17
|
+
at once into RAM. This is beneficial for large files that may not fit into
|
|
18
|
+
available RAM.
|
|
19
|
+
|
|
20
|
+
----------------------------------
|
|
21
|
+
|
|
22
|
+
This [napari] plugin was generated with [copier] using the [napari-plugin-template].
|
|
23
|
+
|
|
24
|
+
<!--
|
|
25
|
+
Don't miss the full getting started guide to set up your new package:
|
|
26
|
+
https://github.com/napari/napari-plugin-template#getting-started
|
|
27
|
+
|
|
28
|
+
and review the napari docs for plugin developers:
|
|
29
|
+
https://napari.org/stable/plugins/index.html
|
|
30
|
+
-->
|
|
31
|
+
|
|
32
|
+
## Installation
|
|
33
|
+
|
|
34
|
+
You can install `napari-memmap-tiff` via [pip]:
|
|
35
|
+
|
|
36
|
+
pip install napari-memmap-tiff
|
|
37
|
+
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
To install latest development version :
|
|
41
|
+
|
|
42
|
+
pip install git+https://github.com/matham/napari-memmap-tiff.git
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
## Contributing
|
|
46
|
+
|
|
47
|
+
Contributions are very welcome. Tests can be run with [tox], please ensure
|
|
48
|
+
the coverage at least stays the same before you submit a pull request.
|
|
49
|
+
|
|
50
|
+
## License
|
|
51
|
+
|
|
52
|
+
Distributed under the terms of the [MIT] license,
|
|
53
|
+
"napari-memmap-tiff" is free and open source software
|
|
54
|
+
|
|
55
|
+
## Issues
|
|
56
|
+
|
|
57
|
+
If you encounter any problems, please [file an issue] along with a detailed description.
|
|
58
|
+
|
|
59
|
+
[napari]: https://github.com/napari/napari
|
|
60
|
+
[copier]: https://copier.readthedocs.io/en/stable/
|
|
61
|
+
[@napari]: https://github.com/napari
|
|
62
|
+
[MIT]: http://opensource.org/licenses/MIT
|
|
63
|
+
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
|
|
64
|
+
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
|
|
65
|
+
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
|
|
66
|
+
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
|
|
67
|
+
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
|
|
68
|
+
[napari-plugin-template]: https://github.com/napari/napari-plugin-template
|
|
69
|
+
|
|
70
|
+
[file an issue]: https://github.com/matham/napari-memmap-tiff/issues
|
|
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|
+
|
|
72
|
+
[napari]: https://github.com/napari/napari
|
|
73
|
+
[tox]: https://tox.readthedocs.io/en/latest/
|
|
74
|
+
[pip]: https://pypi.org/project/pip/
|
|
75
|
+
[PyPI]: https://pypi.org/
|
|
@@ -0,0 +1,121 @@
|
|
|
1
|
+
[project]
|
|
2
|
+
name = "napari-memmap-tiff"
|
|
3
|
+
dynamic = ["version"]
|
|
4
|
+
description = "When installed and enabled in the options, it adds an option that when enabled will make napari load tiffs via memory mapping instead of fully into RAM."
|
|
5
|
+
readme = "README.md"
|
|
6
|
+
license = {file = "LICENSE"}
|
|
7
|
+
authors = [
|
|
8
|
+
{name = "Matthew Einhorn"},
|
|
9
|
+
{email = "matt@einhorn.dev"},
|
|
10
|
+
]
|
|
11
|
+
classifiers = [
|
|
12
|
+
"Development Status :: 2 - Pre-Alpha",
|
|
13
|
+
"Framework :: napari",
|
|
14
|
+
"Intended Audience :: Developers",
|
|
15
|
+
"License :: OSI Approved :: MIT License",
|
|
16
|
+
"Operating System :: OS Independent",
|
|
17
|
+
"Programming Language :: Python",
|
|
18
|
+
"Programming Language :: Python :: 3",
|
|
19
|
+
"Programming Language :: Python :: 3 :: Only",
|
|
20
|
+
"Programming Language :: Python :: 3.10",
|
|
21
|
+
"Programming Language :: Python :: 3.11",
|
|
22
|
+
"Programming Language :: Python :: 3.12",
|
|
23
|
+
"Programming Language :: Python :: 3.13",
|
|
24
|
+
"Topic :: Scientific/Engineering :: Image Processing",
|
|
25
|
+
]
|
|
26
|
+
requires-python = ">=3.10"
|
|
27
|
+
dependencies = [
|
|
28
|
+
"numpy",
|
|
29
|
+
"magicgui",
|
|
30
|
+
"qtpy",
|
|
31
|
+
"scikit-image",
|
|
32
|
+
"tifffile",
|
|
33
|
+
]
|
|
34
|
+
|
|
35
|
+
[project.optional-dependencies]
|
|
36
|
+
testing = [
|
|
37
|
+
"tox",
|
|
38
|
+
"pytest", # https://docs.pytest.org/en/latest/contents.html
|
|
39
|
+
"pytest-cov", # https://pytest-cov.readthedocs.io/en/latest/
|
|
40
|
+
"pytest-qt", # https://pytest-qt.readthedocs.io/en/latest/
|
|
41
|
+
"napari",
|
|
42
|
+
"pyqt5",
|
|
43
|
+
]
|
|
44
|
+
|
|
45
|
+
[project.entry-points."napari.manifest"]
|
|
46
|
+
napari-memmap-tiff = "napari_memmap_tiff:napari.yaml"
|
|
47
|
+
|
|
48
|
+
[project.urls]
|
|
49
|
+
"Bug Tracker" = "https://github.com/matham/napari-memmap-tiff/issues"
|
|
50
|
+
"Documentation" = "https://github.com/matham/napari-memmap-tiff#README.md"
|
|
51
|
+
"Source Code" = "https://github.com/matham/napari-memmap-tiff"
|
|
52
|
+
"User Support" = "https://github.com/matham/napari-memmap-tiff/issues"
|
|
53
|
+
|
|
54
|
+
[build-system]
|
|
55
|
+
requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
|
|
56
|
+
build-backend = "setuptools.build_meta"
|
|
57
|
+
|
|
58
|
+
[tool.setuptools]
|
|
59
|
+
include-package-data = true
|
|
60
|
+
|
|
61
|
+
[tool.setuptools.packages.find]
|
|
62
|
+
where = ["src"]
|
|
63
|
+
|
|
64
|
+
[tool.setuptools.package-data]
|
|
65
|
+
"*" = ["*.yaml"]
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
[tool.setuptools_scm]
|
|
69
|
+
write_to = "src/napari_memmap_tiff/_version.py"
|
|
70
|
+
fallback_version = "0.0.1+nogit"
|
|
71
|
+
|
|
72
|
+
|
|
73
|
+
[tool.black]
|
|
74
|
+
line-length = 79
|
|
75
|
+
target-version = ['py310', 'py311', 'py312', 'py313']
|
|
76
|
+
|
|
77
|
+
[tool.ruff]
|
|
78
|
+
line-length = 79
|
|
79
|
+
lint.select = [
|
|
80
|
+
"E", "F", "W", #flake8
|
|
81
|
+
"UP", # pyupgrade
|
|
82
|
+
"I", # isort
|
|
83
|
+
"BLE", # flake8-blind-exception
|
|
84
|
+
"B", # flake8-bugbear
|
|
85
|
+
"A", # flake8-builtins
|
|
86
|
+
"C4", # flake8-comprehensions
|
|
87
|
+
"ISC", # flake8-implicit-str-concat
|
|
88
|
+
"G", # flake8-logging-format
|
|
89
|
+
"PIE", # flake8-pie
|
|
90
|
+
"SIM", # flake8-simplify
|
|
91
|
+
]
|
|
92
|
+
lint.ignore = [
|
|
93
|
+
"E501", # line too long. let black handle this
|
|
94
|
+
"UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
|
|
95
|
+
"SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
|
|
96
|
+
]
|
|
97
|
+
|
|
98
|
+
exclude = [
|
|
99
|
+
".bzr",
|
|
100
|
+
".direnv",
|
|
101
|
+
".eggs",
|
|
102
|
+
".git",
|
|
103
|
+
".mypy_cache",
|
|
104
|
+
".pants.d",
|
|
105
|
+
".ruff_cache",
|
|
106
|
+
".svn",
|
|
107
|
+
".tox",
|
|
108
|
+
".venv",
|
|
109
|
+
"__pypackages__",
|
|
110
|
+
"_build",
|
|
111
|
+
"buck-out",
|
|
112
|
+
"build",
|
|
113
|
+
"dist",
|
|
114
|
+
"node_modules",
|
|
115
|
+
"venv",
|
|
116
|
+
"*vendored*",
|
|
117
|
+
"*_vendor*",
|
|
118
|
+
]
|
|
119
|
+
|
|
120
|
+
target-version = "py310"
|
|
121
|
+
fix = true
|
|
File without changes
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
from napari_memmap_tiff._widget import memmap_config_widget
|
|
2
|
+
|
|
3
|
+
|
|
4
|
+
def test_memmap_config_widget():
|
|
5
|
+
from imageio.config.plugins import known_plugins
|
|
6
|
+
|
|
7
|
+
widget = memmap_config_widget()
|
|
8
|
+
|
|
9
|
+
widget(True)
|
|
10
|
+
assert "tifffile_memmap" in known_plugins
|
|
11
|
+
widget(False)
|
|
12
|
+
assert "tifffile_memmap" not in known_plugins
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
# file generated by setuptools-scm
|
|
2
|
+
# don't change, don't track in version control
|
|
3
|
+
|
|
4
|
+
__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
|
|
5
|
+
|
|
6
|
+
TYPE_CHECKING = False
|
|
7
|
+
if TYPE_CHECKING:
|
|
8
|
+
from typing import Tuple
|
|
9
|
+
from typing import Union
|
|
10
|
+
|
|
11
|
+
VERSION_TUPLE = Tuple[Union[int, str], ...]
|
|
12
|
+
else:
|
|
13
|
+
VERSION_TUPLE = object
|
|
14
|
+
|
|
15
|
+
version: str
|
|
16
|
+
__version__: str
|
|
17
|
+
__version_tuple__: VERSION_TUPLE
|
|
18
|
+
version_tuple: VERSION_TUPLE
|
|
19
|
+
|
|
20
|
+
__version__ = version = '1.0.0'
|
|
21
|
+
__version_tuple__ = version_tuple = (1, 0, 0)
|
|
@@ -0,0 +1,56 @@
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from typing import TYPE_CHECKING
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import numpy as np
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from imageio.config.extensions import extension_list
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from imageio.config.plugins import PluginConfig, known_plugins
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from imageio.plugins.tifffile_v3 import TifffilePlugin
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from magicgui import magic_factory
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if TYPE_CHECKING:
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pass
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class MemmapTifffilePlugin(TifffilePlugin):
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def read(self, *args, **kwargs) -> np.ndarray:
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return super().read(*args, **kwargs, out="memmap")
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@magic_factory(auto_call=True, persist=False)
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def memmap_config_widget(
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enable_memory_map: bool,
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) -> None:
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"""
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Sets whether to use memory mapping.
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:param enable_memory_map: If enabled, tiff or tif files will be loaded as
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memory mapped data directly from disk, instead of loading it fully into
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memory at once.
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"""
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if enable_memory_map:
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if "tifffile_memmap" in known_plugins:
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return
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known_plugins["tifffile_memmap"] = PluginConfig(
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name="tifffile_memmap",
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class_name="MemmapTifffilePlugin",
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module_name="napari_memmap_tiff._widget",
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is_legacy=False,
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)
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for ext in extension_list:
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if (
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ext.extension in (".tif", ".tiff")
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and "tifffile_memmap" not in ext.priority
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):
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ext.priority.insert(0, "tifffile_memmap")
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else:
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if "tifffile_memmap" not in known_plugins:
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return
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del known_plugins["tifffile_memmap"]
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for ext in extension_list:
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if (
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ext.extension in (".tif", ".tiff")
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and "tifffile_memmap" in ext.priority
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):
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ext.priority.remove("tifffile_memmap")
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name: napari-memmap-tiff
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display_name: Loading tiffs using memory map
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# use 'hidden' to remove plugin from napari hub search results
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visibility: public
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# see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
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categories: ["Annotation", "Segmentation", "Acquisition"]
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contributions:
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commands:
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- id: napari-memmap-tiff.make_function_widget
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python_name: napari_memmap_tiff:memmap_config_widget
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title: Make memmap config widget
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widgets:
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- command: napari-memmap-tiff.make_function_widget
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display_name: Enable / disable memory mapping tiffs
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Metadata-Version: 2.4
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Name: napari-memmap-tiff
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Version: 1.0.0
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Summary: When installed and enabled in the options, it adds an option that when enabled will make napari load tiffs via memory mapping instead of fully into RAM.
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Author: Matthew Einhorn
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Author-email: matt@einhorn.dev
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License:
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The MIT License (MIT)
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Copyright (c) 2025 Matthew Einhorn
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Project-URL: Bug Tracker, https://github.com/matham/napari-memmap-tiff/issues
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Project-URL: Documentation, https://github.com/matham/napari-memmap-tiff#README.md
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Project-URL: Source Code, https://github.com/matham/napari-memmap-tiff
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Project-URL: User Support, https://github.com/matham/napari-memmap-tiff/issues
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Framework :: napari
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Topic :: Scientific/Engineering :: Image Processing
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy
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Requires-Dist: magicgui
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Requires-Dist: qtpy
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Requires-Dist: scikit-image
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Requires-Dist: tifffile
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Provides-Extra: testing
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Requires-Dist: tox; extra == "testing"
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Requires-Dist: pytest; extra == "testing"
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Requires-Dist: pytest-cov; extra == "testing"
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Requires-Dist: pytest-qt; extra == "testing"
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Requires-Dist: napari; extra == "testing"
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Requires-Dist: pyqt5; extra == "testing"
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Dynamic: license-file
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# napari-memmap-tiff
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[](https://github.com/matham/napari-memmap-tiff/raw/main/LICENSE)
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[](https://pypi.org/project/napari-memmap-tiff)
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[](https://python.org)
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[](https://github.com/matham/napari-memmap-tiff/actions)
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[](https://codecov.io/gh/matham/napari-memmap-tiff)
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[](https://napari-hub.org/plugins/napari-memmap-tiff)
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[](https://napari.org/stable/plugins/index.html)
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[](https://github.com/copier-org/copier)
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When installed and enabled in the options, it adds an option that when enabled
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will make napari load tiffs via memory mapping instead of fully into RAM.
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That is, `.tif` and `.tiff` files will be loaded into memory using memory
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mapping, which loads the data directly from disk instead of loading the file
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at once into RAM. This is beneficial for large files that may not fit into
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available RAM.
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----------------------------------
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This [napari] plugin was generated with [copier] using the [napari-plugin-template].
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<!--
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Don't miss the full getting started guide to set up your new package:
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https://github.com/napari/napari-plugin-template#getting-started
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and review the napari docs for plugin developers:
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https://napari.org/stable/plugins/index.html
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-->
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## Installation
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You can install `napari-memmap-tiff` via [pip]:
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pip install napari-memmap-tiff
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To install latest development version :
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pip install git+https://github.com/matham/napari-memmap-tiff.git
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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the coverage at least stays the same before you submit a pull request.
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## License
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Distributed under the terms of the [MIT] license,
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"napari-memmap-tiff" is free and open source software
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## Issues
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If you encounter any problems, please [file an issue] along with a detailed description.
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[napari]: https://github.com/napari/napari
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[copier]: https://copier.readthedocs.io/en/stable/
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[@napari]: https://github.com/napari
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[MIT]: http://opensource.org/licenses/MIT
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[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
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[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
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[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
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[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
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[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
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[napari-plugin-template]: https://github.com/napari/napari-plugin-template
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[file an issue]: https://github.com/matham/napari-memmap-tiff/issues
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[napari]: https://github.com/napari/napari
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[tox]: https://tox.readthedocs.io/en/latest/
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[pip]: https://pypi.org/project/pip/
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[PyPI]: https://pypi.org/
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.gitignore
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.pre-commit-config.yaml
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LICENSE
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MANIFEST.in
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README.md
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pyproject.toml
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tox.ini
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.github/workflows/test_and_deploy.yml
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.napari-hub/DESCRIPTION.md
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.napari-hub/config.yml
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src/napari_memmap_tiff/__init__.py
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src/napari_memmap_tiff/_version.py
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src/napari_memmap_tiff/_widget.py
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src/napari_memmap_tiff/napari.yaml
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src/napari_memmap_tiff.egg-info/PKG-INFO
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src/napari_memmap_tiff.egg-info/SOURCES.txt
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src/napari_memmap_tiff.egg-info/dependency_links.txt
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src/napari_memmap_tiff.egg-info/entry_points.txt
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src/napari_memmap_tiff.egg-info/requires.txt
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src/napari_memmap_tiff.egg-info/top_level.txt
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src/napari_memmap_tiff/_tests/__init__.py
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src/napari_memmap_tiff/_tests/test_widget.py
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@@ -0,0 +1 @@
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@@ -0,0 +1 @@
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napari_memmap_tiff
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# For more information about tox, see https://tox.readthedocs.io/en/latest/
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[tox]
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envlist = py{310,311,312,313}-{linux,macos,windows}
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isolated_build=true
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[gh-actions]
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python =
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3.10: py310
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3.11: py311
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3.12: py312
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3.13: py313
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[gh-actions:env]
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PLATFORM =
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ubuntu-latest: linux
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macos-latest: macos
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windows-latest: windows
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[testenv]
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platform =
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macos: darwin
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linux: linux
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windows: win32
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passenv =
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CI
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GITHUB_ACTIONS
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DISPLAY
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XAUTHORITY
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NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
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PYVISTA_OFF_SCREEN
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extras =
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testing
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commands = pytest -v --color=yes --cov=napari_memmap_tiff --cov-report=xml
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